Variant report

Variant	rs71539408
Chromosome Location	chr12:21654825-21654826
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr12:21653870-21654922	GM19099	blood:	n/a	chr12:21654813-21654822 chr12:21654813-21654822
2	YY1	chr12:21654602-21654876	K562	blood:	n/a	n/a
3	POLR2A	chr12:21654030-21655069	HUVEC	blood vessel:	n/a	n/a
4	TAF7	chr12:21654272-21655132	H1-hESC	embryonic stem cell:	n/a	n/a
5	PML	chr12:21653797-21655149	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:21653822-21655246	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr12:21653812-21655229	GM12878	blood:	n/a	n/a
8	HEY1	chr12:21654246-21654956	K562	blood:	n/a	n/a
9	GABPA	chr12:21653982-21654953	HL-60	blood:	n/a	n/a
10	EP300	chr12:21654122-21654974	A549	lung:	n/a	n/a
11	MXI1	chr12:21653867-21655482	GM12878	blood:	n/a	n/a
12	CEBPB	chr12:21654022-21654960	GM12878	blood:	n/a	chr12:21654590-21654598
13	ELF1	chr12:21654091-21655094	MCF-7	breast:	n/a	n/a
14	POLR2A	chr12:21653554-21655298	PBDE	blood:	n/a	n/a
15	MAX	chr12:21654016-21655355	ECC-1	luminal epithelium:	n/a	chr12:21654901-21654911
16	BRCA1	chr12:21654299-21654864	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:21653823-21655422	GM12878	blood:	n/a	n/a
18	E2F6	chr12:21653778-21655202	K562	blood:	n/a	chr12:21654540-21654552 chr12:21654589-21654598 chr12:21654539-21654550
19	POLR2A	chr12:21654163-21655078	A549	lung:	n/a	n/a
20	E2F6	chr12:21654074-21654972	A549	lung:	n/a	chr12:21654540-21654552 chr12:21654589-21654598 chr12:21654539-21654550
21	MXI1	chr12:21653059-21655687	SK-N-SH	brain:	n/a	n/a
22	HEY1	chr12:21654162-21654987	K562	blood:	n/a	n/a
23	MAFK	chr12:21654209-21654952	HepG2	liver:	n/a	n/a
24	MAX	chr12:21654049-21655020	MCF-7	breast:	n/a	chr12:21654901-21654911
25	MYC	chr12:21653866-21655507	NB4	blood:	n/a	chr12:21654901-21654911
26	ELF1	chr12:21654334-21655087	K562	blood:	n/a	n/a
27	PML	chr12:21654271-21654998	K562	blood:	n/a	n/a
28	POLR2A	chr12:21653840-21655197	Hela-S3	cervix:	n/a	n/a
29	RUNX3	chr12:21653894-21654915	GM12878	blood:	n/a	n/a
30	ELF1	chr12:21653990-21655048	HepG2	liver:	n/a	n/a
31	POLR2A	chr12:21654655-21654877	HepG2	liver:	n/a	n/a
32	MAX	chr12:21654007-21654958	SK-N-SH	brain:	n/a	chr12:21654901-21654911
33	IRF1	chr12:21654333-21654872	K562	blood:	n/a	chr12:21654589-21654598
34	TAF1	chr12:21654636-21654935	Hela-S3	cervix:	n/a	n/a
35	MAX	chr12:21653853-21655344	Hela-S3	cervix:	n/a	chr12:21654901-21654911
36	REST	chr12:21654146-21655179	HL-60	blood:	n/a	chr12:21654821-21654831 chr12:21654813-21654833 chr12:21654300-21654313 chr12:21654834-21654843 chr12:21654813-21654833
37	GABPA	chr12:21653841-21655076	A549	lung:	n/a	n/a
38	POLR2A	chr12:21654176-21655355	HepG2	liver:	n/a	n/a
39	PML	chr12:21654054-21654831	GM12878	blood:	n/a	n/a
40	E2F6	chr12:21654196-21654974	H1-hESC	embryonic stem cell:	n/a	chr12:21654540-21654552 chr12:21654589-21654598 chr12:21654539-21654550
41	MAX	chr12:21653898-21655123	Hela-S3	cervix:	n/a	chr12:21654901-21654911
42	MYC	chr12:21654062-21654916	MCF10A-Er-Src	breast:	n/a	chr12:21654901-21654911
43	POLR2A	chr12:21654000-21655390	ECC-1	luminal epithelium:	n/a	n/a
44	JUND	chr12:21654219-21655198	A549	lung:	n/a	chr12:21654591-21654600 chr12:21654275-21654284
45	FOS	chr12:21654441-21654835	Hela-S3	cervix:	n/a	chr12:21654591-21654600
46	MAX	chr12:21654109-21655094	HepG2	liver:	n/a	chr12:21654901-21654911
47	YY1	chr12:21654097-21655001	SK-N-SH	brain:	n/a	chr12:21654946-21654955
48	MTA3	chr12:21653955-21654912	GM12878	blood:	n/a	n/a
49	CHD2	chr12:21653952-21654940	Hela-S3	cervix:	n/a	n/a
50	SIN3AK20	chr12:21654045-21654968	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:21654795-21654845	NH-A	brain:	n/a
2	chr12:21654795-21654845	HIPEpiC	eye:	n/a
3	chr12:21654795-21654845	NHBE	bronchial:	n/a
4	chr12:21654795-21654845	HEK293	kidney:	embryo
5	chr12:21654795-21654845	CMK	blood:	n/a
6	chr12:21654795-21654845	NT2-D1	testis:	n/a
7	chr12:21654795-21654845	PANC-1	pancreas:	n/a
8	chr12:21654795-21654845	HEEpiC	esophagus:	n/a
9	chr12:21654795-21654845	HRE	kidney:	n/a
10	chr12:21654795-21654845	RPTEC	kidney:	n/a
11	chr12:21654795-21654845	PrEC	prostate:	n/a
12	chr12:21654795-21654845	ECC-1	luminal epithelium:	n/a
13	chr12:21654795-21654845	HNPCEpiC	eye:	n/a
14	chr12:21654795-21654845	Hela-S3	cervix:	n/a
15	chr12:21654795-21654845	MCF-7	breast:	n/a
16	chr12:21654795-21654845	GM19239	blood:	n/a
17	chr12:21654795-21654845	AG09309	skin:	n/a
18	chr12:21654795-21654845	HCF	heart:	n/a
19	chr12:21654795-21654845	GM12878	blood:	n/a
20	chr12:21654795-21654845	MCF10A-Er-Src	breast:	n/a
21	chr12:21654795-21654845	SK-N-SH	brain:	n/a
22	chr12:21654795-21654845	PFSK-1	brain:	n/a
23	chr12:21654795-21654845	SAEC	small airway:	n/a
24	chr12:21654795-21654845	AG04449	skin:	fetal
25	chr12:21654795-21654845	HCM	heart:	n/a
26	chr12:21654795-21654845	HCPEpiC	choroid plexus:	n/a
27	chr12:21654795-21654845	AG04450	lung:	fetal
28	chr12:21654795-21654845	HPAEpiC	pulmonary alveolar:	n/a
29	chr12:21654795-21654845	SK-N-SH_RA	brain:	n/a
30	chr12:21654795-21654845	HL-60	blood:	n/a
31	chr12:21654795-21654845	HAEpiC	amniotic membrane:	n/a
32	chr12:21654795-21654845	U87	brain:	n/a
33	chr12:21654795-21654845	Caco-2	colon:	n/a
34	chr12:21654795-21654845	NHDF-neo	bronchial:	n/a
35	chr12:21654795-21654845	HRPEpiC	eye:	n/a
36	chr12:21654795-21654845	K562	blood:	n/a
37	chr12:21654795-21654845	HepG2	liver:	n/a
38	chr12:21654795-21654845	HRCEpiC	kidney:	n/a
39	chr12:21654795-21654845	GM12891	blood:	n/a
40	chr12:21654795-21654845	NB4	blood:	n/a
41	chr12:21654795-21654845	Jurkat	blood:	n/a
42	chr12:21654795-21654845	BJ	skin:	n/a
43	chr12:21654795-21654845	SK-N-MC	brain:	n/a
44	chr12:21654795-21654845	AG09319	gingival:	n/a
45	chr12:21654795-21654845	HUVEC	blood vessel:	n/a
46	chr12:21654795-21654845	HMEC	breast:	n/a
47	chr12:21654795-21654845	ProgFib	skin:	n/a
48	chr12:21654795-21654845	BE2_C	brain:	n/a
49	chr12:21654795-21654845	Hepatocyte	liver:	n/a
50	chr12:21654795-21654845	SKMC	muscle:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:21654617..21655263-chr12:57481242..57482048,2	Hela-S3	cervix:
2	chr12:21654296..21655290-chr9:135819833..135820422,2	Hela-S3	cervix:
3	chr1:9188306..9189002-chr12:21654516..21655344,2	Hela-S3	cervix:
4	chr12:21653197..21655257-chr12:21809726..21811694,2	K562	blood:
5	chr12:21654284..21655120-chr5:158636468..158637131,2	Hela-S3	cervix:
6	chr12:21653863..21655490-chr12:22198033..22200548,2	MCF-7	breast:

Variant related genes	Relation type
RECQL	TF binding region
RECQL	CpG island
ENSG00000253256	Chromatin interaction
ENSG00000111716	Chromatin interaction
ENSG00000165699	Chromatin interaction
ENSG00000166881	Chromatin interaction
ENSG00000145860	Chromatin interaction
ENSG00000111726	Chromatin interaction
ENSG00000180758	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10492116	1.00[AFR][1000 genomes]
rs11835261	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17627175	0.83[EUR][1000 genomes]
rs17627561	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17627677	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17682057	1.00[AFR][1000 genomes]
rs17684048	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71539409	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71539410	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71581963	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71581964	0.83[EUR][1000 genomes]
rs71581965	0.83[EUR][1000 genomes]
rs71582885	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898896	chr12:21561645-21695584	Strong transcription Bivalent Enhancer Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1043936	chr12:21562673-21979030	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv557741	chr12:21578559-22169854	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1054220	chr12:21612158-21692103	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1036084	chr12:21631009-21792756	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21652600-21656200	Active TSS	NHLF	lung
2	chr12:21652800-21655800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:21652800-21656000	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr12:21652800-21656000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:21652800-21656000	Active TSS	Right Atrium	heart
6	chr12:21652800-21656400	Active TSS	Psoas Muscle	Psoas
7	chr12:21653000-21655800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:21653000-21656000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr12:21653000-21656000	Active TSS	Right Ventricle	heart
10	chr12:21653000-21656000	Active TSS	K562	blood
11	chr12:21653000-21656200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:21653000-21656200	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr12:21653200-21655400	Active TSS	Fetal Kidney	kidney
14	chr12:21653200-21655800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:21653200-21655800	Active TSS	Ovary	ovary
16	chr12:21653400-21655600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr12:21653400-21655600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:21653400-21655800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:21653400-21656000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr12:21653400-21656000	Active TSS	NHDF-Ad	bronchial
21	chr12:21653600-21655600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:21653600-21655600	Active TSS	Left Ventricle	heart
23	chr12:21653600-21655600	Active TSS	Lung	lung
24	chr12:21653600-21655600	Bivalent/Poised TSS	HepG2	liver
25	chr12:21653600-21655800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr12:21653600-21655800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:21653600-21655800	Active TSS	Fetal Muscle Trunk	muscle
28	chr12:21653600-21656000	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr12:21653600-21656400	Active TSS	HUES48 Cell Line	embryonic stem cell
30	chr12:21653800-21655200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:21653800-21655400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:21653800-21655400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr12:21653800-21655400	Active TSS	Fetal Brain Male	brain
34	chr12:21653800-21655600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr12:21653800-21655600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr12:21653800-21655600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:21653800-21655600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr12:21653800-21655600	Active TSS	Brain Germinal Matrix	brain
39	chr12:21653800-21655600	Active TSS	Colon Smooth Muscle	Colon
40	chr12:21653800-21655600	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr12:21653800-21655600	Active TSS	Fetal Intestine Small	intestine
42	chr12:21653800-21655800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:21653800-21655800	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr12:21653800-21655800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:21653800-21655800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:21653800-21655800	Active TSS	Fetal Stomach	stomach
47	chr12:21653800-21655800	Active TSS	A549	lung
48	chr12:21653800-21655800	Active TSS	GM12878-XiMat	blood
49	chr12:21653800-21655800	Active TSS	HSMM	muscle
50	chr12:21653800-21655800	Active TSS	NH-A	brain

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